Evidence map›Paper›PMID 36265467›Full record

ArticleCell systems2022

ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data.

Michael K B Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett and 15 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.8field-weighted citation impact, top 29% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 12 citations in OpenAlex.

  1. Article
  2. A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
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  4. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors at 8 institutions in 2 countries.

Michael K B FordNational Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: mike.ford@nih.gov.
Ananth HariNational Cancer Institute, NIH, Bethesda, MD, USA; Department of Electrical Engineering, University of Maryland, College Park, MD, USA.
Oscar RodriguezDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
Junyan XuNational Cancer Institute, NIH, Bethesda, MD, USA.
Justin LackNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Cihan OguzNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Yu ZhangNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Sarah WeberNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Mary MaglioccoNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Jason BarnettNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Sandhya XirasagarNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Smilee SamuelNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Luisa ImbertiDiagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy.
Paolo BonfantiUniversity of Milano-Bicocca, Fondazione MBBM, Monza, Italy.
Andrea BiondiUniversity of Milano-Bicocca, Fondazione MBBM, Monza, Italy.
Clifton L DalgardUniformed Services University of the Health Sciences, Bethesda, MD, USA.
Stephen ChanockNational Cancer Institute, NIH, Bethesda, MD, USA.
Lindsey RosenNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Steven HollandNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Helen SuNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
Luigi NotarangeloNational Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
NIAID COVID Consortium
Uzi VishkinDepartment of Electrical Engineering, University of Maryland, College Park, MD, USA.
Corey T WatsonDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
S Cenk SahinalpNational Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: cenk.sahinalp@nih.gov.
National Institute of Allergy and Infectious Diseases · USNational Cancer Institute · USUniversity of Louisville · USUniversity of Maryland, College Park · USUniversity of Milano-Bicocca · ITAzienda Socio Sanitaria Territoriale degli Spedali Civili di Brescia · ITNational Institutes of Health · USUniformed Services University of the Health Sciences · US

Funding

Tumor evolution and intratumor heterogeneityZIABC011987 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI SAHINALP, SULEYMAN · 2020 to 2025
$6.6M
Intramural NIH HHS ZIA BC011987
6 · The paper itself

Abstract

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which are critical for the structure of antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype when using standard short-read sequencing technologies. Here, we introduce ImmunoTyper-SR, an algorithmic tool for the genotyping and CNV analysis of the germline IGHV genes on Illumina whole-genome sequencing (WGS) data using a combinatorial optimization formulation that resolves ambiguous read mappings. We have validated ImmunoTyper-SR on 12 individuals, whose IGHV allele composition had been independently validated, as well as concordance between WGS replicates from nine individuals. We then applied ImmunoTyper-SR on 585 COVID patients to investigate the associations between IGHV alleles and anti-type I IFN autoantibodies, which were previously associated with COVID-19 severity.

Indexed as

COVID-19Immunoglobulin Variable RegionAutoantibodiesGenotypeHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsAutoantibodiesImmunoglobulin Heavy ChainsImmunoglobulin Variable Regionalgorithmscomputational biologygenomicsgenotypingILPimmunogenomicsimmunoglobulinnext generation sequencingoptimizationWGS

Identifiers

PMID36265467
PMCPMC10084889
OpenAlexW4306851567

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.